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[jabaws.git] / binaries / src / ViennaRNA / doc / latex / group__eval.tex
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+\hypertarget{group__eval}{\section{Energy evaluation}
+\label{group__eval}\index{Energy evaluation@{Energy evaluation}}
+}
+
+
+This module contains all functions and variables related to energy evaluation of sequence/structure pairs.  
+
+
+Collaboration diagram for Energy evaluation\-:
+\nopagebreak
+\begin{figure}[H]
+\begin{center}
+\leavevmode
+\includegraphics[width=336pt]{group__eval}
+\end{center}
+\end{figure}
+\subsection*{Functions}
+\begin{DoxyCompactItemize}
+\item 
+float \hyperlink{group__eval_gaf93986cb3cb29770ec9cca69c9fab8cf}{energy\-\_\-of\-\_\-structure} (const char $\ast$string, const char $\ast$structure, int verbosity\-\_\-level)
+\begin{DoxyCompactList}\small\item\em Calculate the free energy of an already folded R\-N\-A using global model detail settings. \end{DoxyCompactList}\item 
+float \hyperlink{group__eval_gab5169ea4f72f250e43811463a33f4e40}{energy\-\_\-of\-\_\-struct\-\_\-par} (const char $\ast$string, const char $\ast$structure, \hyperlink{structparamT}{param\-T} $\ast$parameters, int verbosity\-\_\-level)
+\begin{DoxyCompactList}\small\item\em Calculate the free energy of an already folded R\-N\-A. \end{DoxyCompactList}\item 
+float \hyperlink{group__eval_gaeb14f3664aec67fc03268ac75253f0f8}{energy\-\_\-of\-\_\-circ\-\_\-structure} (const char $\ast$string, const char $\ast$structure, int verbosity\-\_\-level)
+\begin{DoxyCompactList}\small\item\em Calculate the free energy of an already folded circular R\-N\-A. \end{DoxyCompactList}\item 
+float \hyperlink{group__eval_ga75dc765ee4a1177832bc817c94cf88e5}{energy\-\_\-of\-\_\-circ\-\_\-struct\-\_\-par} (const char $\ast$string, const char $\ast$structure, \hyperlink{structparamT}{param\-T} $\ast$parameters, int verbosity\-\_\-level)
+\begin{DoxyCompactList}\small\item\em Calculate the free energy of an already folded circular R\-N\-A. \end{DoxyCompactList}\item 
+int \hyperlink{group__eval_ga8831445966b761417e713360791299d8}{energy\-\_\-of\-\_\-structure\-\_\-pt} (const char $\ast$string, short $\ast$ptable, short $\ast$s, short $\ast$s1, int verbosity\-\_\-level)
+\begin{DoxyCompactList}\small\item\em Calculate the free energy of an already folded R\-N\-A. \end{DoxyCompactList}\item 
+int \hyperlink{group__eval_gada4701dd7519b29da75ceac147601f4e}{energy\-\_\-of\-\_\-struct\-\_\-pt\-\_\-par} (const char $\ast$string, short $\ast$ptable, short $\ast$s, short $\ast$s1, \hyperlink{structparamT}{param\-T} $\ast$parameters, int verbosity\-\_\-level)
+\begin{DoxyCompactList}\small\item\em Calculate the free energy of an already folded R\-N\-A. \end{DoxyCompactList}\end{DoxyCompactItemize}
+\subsection*{Variables}
+\begin{DoxyCompactItemize}
+\item 
+\hypertarget{group__eval_ga567530678f6260a1a649a5beca5da4c5}{int \hyperlink{group__eval_ga567530678f6260a1a649a5beca5da4c5}{eos\-\_\-debug}}\label{group__eval_ga567530678f6260a1a649a5beca5da4c5}
+
+\begin{DoxyCompactList}\small\item\em verbose info from energy\-\_\-of\-\_\-struct \end{DoxyCompactList}\end{DoxyCompactItemize}
+
+
+\subsection{Detailed Description}
+This module contains all functions and variables related to energy evaluation of sequence/structure pairs. 
+
+\subsection{Function Documentation}
+\hypertarget{group__eval_gaf93986cb3cb29770ec9cca69c9fab8cf}{\index{Energy evaluation@{Energy evaluation}!energy\-\_\-of\-\_\-structure@{energy\-\_\-of\-\_\-structure}}
+\index{energy\-\_\-of\-\_\-structure@{energy\-\_\-of\-\_\-structure}!Energy evaluation@{Energy evaluation}}
+\subsubsection[{energy\-\_\-of\-\_\-structure}]{\setlength{\rightskip}{0pt plus 5cm}float energy\-\_\-of\-\_\-structure (
+\begin{DoxyParamCaption}
+\item[{const char $\ast$}]{string, }
+\item[{const char $\ast$}]{structure, }
+\item[{int}]{verbosity\-\_\-level}
+\end{DoxyParamCaption}
+)}}\label{group__eval_gaf93986cb3cb29770ec9cca69c9fab8cf}
+
+
+Calculate the free energy of an already folded R\-N\-A using global model detail settings. 
+
+If verbosity level is set to a value $>$0, energies of structure elements are printed to stdout
+
+\begin{DoxyNote}{Note}
+Open\-M\-P\-: This function relies on several global model settings variables and thus is not to be considered threadsafe. See \hyperlink{group__eval_gab5169ea4f72f250e43811463a33f4e40}{energy\-\_\-of\-\_\-struct\-\_\-par()} for a completely threadsafe implementation.
+\end{DoxyNote}
+\begin{DoxySeeAlso}{See Also}
+\hyperlink{group__eval_gab5169ea4f72f250e43811463a33f4e40}{energy\-\_\-of\-\_\-struct\-\_\-par()}, \hyperlink{group__eval_gaeb14f3664aec67fc03268ac75253f0f8}{energy\-\_\-of\-\_\-circ\-\_\-structure()}
+\end{DoxySeeAlso}
+
+\begin{DoxyParams}{Parameters}
+{\em string} & R\-N\-A sequence \\
+\hline
+{\em structure} & secondary structure in dot-\/bracket notation \\
+\hline
+{\em verbosity\-\_\-level} & a flag to turn verbose output on/off \\
+\hline
+\end{DoxyParams}
+\begin{DoxyReturn}{Returns}
+the free energy of the input structure given the input sequence in kcal/mol 
+\end{DoxyReturn}
+\hypertarget{group__eval_gab5169ea4f72f250e43811463a33f4e40}{\index{Energy evaluation@{Energy evaluation}!energy\-\_\-of\-\_\-struct\-\_\-par@{energy\-\_\-of\-\_\-struct\-\_\-par}}
+\index{energy\-\_\-of\-\_\-struct\-\_\-par@{energy\-\_\-of\-\_\-struct\-\_\-par}!Energy evaluation@{Energy evaluation}}
+\subsubsection[{energy\-\_\-of\-\_\-struct\-\_\-par}]{\setlength{\rightskip}{0pt plus 5cm}float energy\-\_\-of\-\_\-struct\-\_\-par (
+\begin{DoxyParamCaption}
+\item[{const char $\ast$}]{string, }
+\item[{const char $\ast$}]{structure, }
+\item[{{\bf param\-T} $\ast$}]{parameters, }
+\item[{int}]{verbosity\-\_\-level}
+\end{DoxyParamCaption}
+)}}\label{group__eval_gab5169ea4f72f250e43811463a33f4e40}
+
+
+Calculate the free energy of an already folded R\-N\-A. 
+
+If verbosity level is set to a value $>$0, energies of structure elements are printed to stdout
+
+\begin{DoxySeeAlso}{See Also}
+\hyperlink{group__eval_gaeb14f3664aec67fc03268ac75253f0f8}{energy\-\_\-of\-\_\-circ\-\_\-structure()}, \hyperlink{group__eval_ga8831445966b761417e713360791299d8}{energy\-\_\-of\-\_\-structure\-\_\-pt()}, \hyperlink{group__energy__parameters_gac2f3ca440b7eaf4d999fb27da949fe72}{get\-\_\-scaled\-\_\-parameters()}
+\end{DoxySeeAlso}
+
+\begin{DoxyParams}{Parameters}
+{\em string} & R\-N\-A sequence in uppercase letters \\
+\hline
+{\em structure} & Secondary structure in dot-\/bracket notation \\
+\hline
+{\em parameters} & A data structure containing the prescaled energy contributions and the model details. \\
+\hline
+{\em verbosity\-\_\-level} & A flag to turn verbose output on/off \\
+\hline
+\end{DoxyParams}
+\begin{DoxyReturn}{Returns}
+The free energy of the input structure given the input sequence in kcal/mol 
+\end{DoxyReturn}
+\hypertarget{group__eval_gaeb14f3664aec67fc03268ac75253f0f8}{\index{Energy evaluation@{Energy evaluation}!energy\-\_\-of\-\_\-circ\-\_\-structure@{energy\-\_\-of\-\_\-circ\-\_\-structure}}
+\index{energy\-\_\-of\-\_\-circ\-\_\-structure@{energy\-\_\-of\-\_\-circ\-\_\-structure}!Energy evaluation@{Energy evaluation}}
+\subsubsection[{energy\-\_\-of\-\_\-circ\-\_\-structure}]{\setlength{\rightskip}{0pt plus 5cm}float energy\-\_\-of\-\_\-circ\-\_\-structure (
+\begin{DoxyParamCaption}
+\item[{const char $\ast$}]{string, }
+\item[{const char $\ast$}]{structure, }
+\item[{int}]{verbosity\-\_\-level}
+\end{DoxyParamCaption}
+)}}\label{group__eval_gaeb14f3664aec67fc03268ac75253f0f8}
+
+
+Calculate the free energy of an already folded circular R\-N\-A. 
+
+\begin{DoxyNote}{Note}
+Open\-M\-P\-: This function relies on several global model settings variables and thus is not to be considered threadsafe. See \hyperlink{group__eval_ga75dc765ee4a1177832bc817c94cf88e5}{energy\-\_\-of\-\_\-circ\-\_\-struct\-\_\-par()} for a completely threadsafe implementation.
+\end{DoxyNote}
+If verbosity level is set to a value $>$0, energies of structure elements are printed to stdout
+
+\begin{DoxySeeAlso}{See Also}
+\hyperlink{group__eval_ga75dc765ee4a1177832bc817c94cf88e5}{energy\-\_\-of\-\_\-circ\-\_\-struct\-\_\-par()}, \hyperlink{group__eval_gab5169ea4f72f250e43811463a33f4e40}{energy\-\_\-of\-\_\-struct\-\_\-par()}
+\end{DoxySeeAlso}
+
+\begin{DoxyParams}{Parameters}
+{\em string} & R\-N\-A sequence \\
+\hline
+{\em structure} & Secondary structure in dot-\/bracket notation \\
+\hline
+{\em verbosity\-\_\-level} & A flag to turn verbose output on/off \\
+\hline
+\end{DoxyParams}
+\begin{DoxyReturn}{Returns}
+The free energy of the input structure given the input sequence in kcal/mol 
+\end{DoxyReturn}
+\hypertarget{group__eval_ga75dc765ee4a1177832bc817c94cf88e5}{\index{Energy evaluation@{Energy evaluation}!energy\-\_\-of\-\_\-circ\-\_\-struct\-\_\-par@{energy\-\_\-of\-\_\-circ\-\_\-struct\-\_\-par}}
+\index{energy\-\_\-of\-\_\-circ\-\_\-struct\-\_\-par@{energy\-\_\-of\-\_\-circ\-\_\-struct\-\_\-par}!Energy evaluation@{Energy evaluation}}
+\subsubsection[{energy\-\_\-of\-\_\-circ\-\_\-struct\-\_\-par}]{\setlength{\rightskip}{0pt plus 5cm}float energy\-\_\-of\-\_\-circ\-\_\-struct\-\_\-par (
+\begin{DoxyParamCaption}
+\item[{const char $\ast$}]{string, }
+\item[{const char $\ast$}]{structure, }
+\item[{{\bf param\-T} $\ast$}]{parameters, }
+\item[{int}]{verbosity\-\_\-level}
+\end{DoxyParamCaption}
+)}}\label{group__eval_ga75dc765ee4a1177832bc817c94cf88e5}
+
+
+Calculate the free energy of an already folded circular R\-N\-A. 
+
+If verbosity level is set to a value $>$0, energies of structure elements are printed to stdout
+
+\begin{DoxySeeAlso}{See Also}
+\hyperlink{group__eval_gab5169ea4f72f250e43811463a33f4e40}{energy\-\_\-of\-\_\-struct\-\_\-par()}, \hyperlink{group__energy__parameters_gac2f3ca440b7eaf4d999fb27da949fe72}{get\-\_\-scaled\-\_\-parameters()}
+\end{DoxySeeAlso}
+
+\begin{DoxyParams}{Parameters}
+{\em string} & R\-N\-A sequence \\
+\hline
+{\em structure} & Secondary structure in dot-\/bracket notation \\
+\hline
+{\em parameters} & A data structure containing the prescaled energy contributions and the model details. \\
+\hline
+{\em verbosity\-\_\-level} & A flag to turn verbose output on/off \\
+\hline
+\end{DoxyParams}
+\begin{DoxyReturn}{Returns}
+The free energy of the input structure given the input sequence in kcal/mol 
+\end{DoxyReturn}
+\hypertarget{group__eval_ga8831445966b761417e713360791299d8}{\index{Energy evaluation@{Energy evaluation}!energy\-\_\-of\-\_\-structure\-\_\-pt@{energy\-\_\-of\-\_\-structure\-\_\-pt}}
+\index{energy\-\_\-of\-\_\-structure\-\_\-pt@{energy\-\_\-of\-\_\-structure\-\_\-pt}!Energy evaluation@{Energy evaluation}}
+\subsubsection[{energy\-\_\-of\-\_\-structure\-\_\-pt}]{\setlength{\rightskip}{0pt plus 5cm}int energy\-\_\-of\-\_\-structure\-\_\-pt (
+\begin{DoxyParamCaption}
+\item[{const char $\ast$}]{string, }
+\item[{short $\ast$}]{ptable, }
+\item[{short $\ast$}]{s, }
+\item[{short $\ast$}]{s1, }
+\item[{int}]{verbosity\-\_\-level}
+\end{DoxyParamCaption}
+)}}\label{group__eval_ga8831445966b761417e713360791299d8}
+
+
+Calculate the free energy of an already folded R\-N\-A. 
+
+If verbosity level is set to a value $>$0, energies of structure elements are printed to stdout
+
+\begin{DoxyNote}{Note}
+Open\-M\-P\-: This function relies on several global model settings variables and thus is not to be considered threadsafe. See \hyperlink{group__eval_gada4701dd7519b29da75ceac147601f4e}{energy\-\_\-of\-\_\-struct\-\_\-pt\-\_\-par()} for a completely threadsafe implementation.
+\end{DoxyNote}
+\begin{DoxySeeAlso}{See Also}
+\hyperlink{utils_8h_a89c32307ee50a0026f4a3131fac0845a}{make\-\_\-pair\-\_\-table()}, \hyperlink{group__eval_gada4701dd7519b29da75ceac147601f4e}{energy\-\_\-of\-\_\-struct\-\_\-pt\-\_\-par()}
+\end{DoxySeeAlso}
+
+\begin{DoxyParams}{Parameters}
+{\em string} & R\-N\-A sequence \\
+\hline
+{\em ptable} & the pair table of the secondary structure \\
+\hline
+{\em s} & encoded R\-N\-A sequence \\
+\hline
+{\em s1} & encoded R\-N\-A sequence \\
+\hline
+{\em verbosity\-\_\-level} & a flag to turn verbose output on/off \\
+\hline
+\end{DoxyParams}
+\begin{DoxyReturn}{Returns}
+the free energy of the input structure given the input sequence in 10kcal/mol 
+\end{DoxyReturn}
+\hypertarget{group__eval_gada4701dd7519b29da75ceac147601f4e}{\index{Energy evaluation@{Energy evaluation}!energy\-\_\-of\-\_\-struct\-\_\-pt\-\_\-par@{energy\-\_\-of\-\_\-struct\-\_\-pt\-\_\-par}}
+\index{energy\-\_\-of\-\_\-struct\-\_\-pt\-\_\-par@{energy\-\_\-of\-\_\-struct\-\_\-pt\-\_\-par}!Energy evaluation@{Energy evaluation}}
+\subsubsection[{energy\-\_\-of\-\_\-struct\-\_\-pt\-\_\-par}]{\setlength{\rightskip}{0pt plus 5cm}int energy\-\_\-of\-\_\-struct\-\_\-pt\-\_\-par (
+\begin{DoxyParamCaption}
+\item[{const char $\ast$}]{string, }
+\item[{short $\ast$}]{ptable, }
+\item[{short $\ast$}]{s, }
+\item[{short $\ast$}]{s1, }
+\item[{{\bf param\-T} $\ast$}]{parameters, }
+\item[{int}]{verbosity\-\_\-level}
+\end{DoxyParamCaption}
+)}}\label{group__eval_gada4701dd7519b29da75ceac147601f4e}
+
+
+Calculate the free energy of an already folded R\-N\-A. 
+
+If verbosity level is set to a value $>$0, energies of structure elements are printed to stdout
+
+\begin{DoxySeeAlso}{See Also}
+\hyperlink{utils_8h_a89c32307ee50a0026f4a3131fac0845a}{make\-\_\-pair\-\_\-table()}, \hyperlink{group__eval_gab5169ea4f72f250e43811463a33f4e40}{energy\-\_\-of\-\_\-struct\-\_\-par()}, \hyperlink{group__energy__parameters_gac2f3ca440b7eaf4d999fb27da949fe72}{get\-\_\-scaled\-\_\-parameters()}
+\end{DoxySeeAlso}
+
+\begin{DoxyParams}{Parameters}
+{\em string} & R\-N\-A sequence in uppercase letters \\
+\hline
+{\em ptable} & The pair table of the secondary structure \\
+\hline
+{\em s} & Encoded R\-N\-A sequence \\
+\hline
+{\em s1} & Encoded R\-N\-A sequence \\
+\hline
+{\em parameters} & A data structure containing the prescaled energy contributions and the model details. \\
+\hline
+{\em verbosity\-\_\-level} & A flag to turn verbose output on/off \\
+\hline
+\end{DoxyParams}
+\begin{DoxyReturn}{Returns}
+The free energy of the input structure given the input sequence in 10kcal/mol 
+\end{DoxyReturn}